• James T. Kirk: William Shatner
• Spock: Leonard Nimoy
• Leonard "Bones" McCoy: Deforest Kelley
• Chekov: Walter Koenig
• Sulu: George Takei
• Uhura: Nichelle Nichols
• Kruge : Christopher Lloyd
• Lt. Saavik: Robin Curtis
• Dr. David Marcus: Merritt Butrick
• Vulcan High Priestess: Dame Judith Anderson
• Klingon Prisoner: John Larroquette

Heading home, the Enterprise receives no replies from Starfleet regarding the Genesis planet. Most of the trainees have been reassigned to other ships by now, and Kirk is still mourning the death of Spock. Arriving at space dock, the crew also sees the USS Excelsior, a ship much larger than the Enterprise which has the faster transwarp propulsion system. But before the ship can rest easy, someone breaks into Spock's cabin, which Kirk had declared off-limits. Kirk goes there himself and hears Spock's voice asking why his body was left on the Genesis planet. Kirk finds that McCoy, on the edge of a nervous breakdown, is the trespasser. On arrival, Admiral Morrow reveals that the Enterprise is to be decommissioned instead of repaired, and also tells the crew that the Genesis device has become a hot topic in the Federation and a topic not to be discussed openly. Scotty is made Captain of engineering for the Excelsior, and the rest of the crew are promised extended leave.

Klingon Captain Kruuge, having obtained an illegal copy of the Genesis proposal from a pirate vessel (which he then destroyed), orders his ship, a new Klingon Bird of Prey armed with a cloaking device, to the Genesis planet to investigate the device's potential as a weapon for the Klingons. At the same time, the USS Grissom, with its new science officer Saavik and Genesis specialist David Marcus, arrives at the planet and detects life signs near the torpedo tube in which Spock's body had been disposed.

Kirk and his officers, minus the hospitalized McCoy, relax at Kirk's home when Sarek, Spock's father, visits. Sarek mind-melds with Kirk in search of Spock's katra - his spirit. Revealing that Vulcans can pass their spirits on to others when their bodies are near death, Sarek admits that Kirk does not possess Spock's spirit. Kirk checks ship's logs and sees that Spock did, in fact, pass his katra on - to McCoy. Sarek tells him that McCoy must be taken to Vulcan so that Spock can be released into a body of his own.

After arguing with Captain Esteban, Saavik and David get permission to beam down, where they find that the life form is a kind of giant slug, probably having developed from microbes on the torpedo's surface. But they also find the body of Spock missing, and the planet seems very unstable, with extreme weather conditions isolated in random geological locations.

Kirk tries to get permission from Admiral Morrow to return to Genesis and retrieve Spock's body, but is unable to convince Morrow of the validity of Vulcan mysticism. McCoy, in the meantime, tries to hire a private ship from an alien merchant in a bar, but is removed by Starfleet agents when he begins to argue loudly with the alien about going to Genesis. McCoy is put in detention, where Kirk visits him, and, with Sulu's help, distracts the guards and smuggles McCoy out of the holding area. Uhura, having taken an assignment at a transporter station, beams Kirk, McCoy and Sulu to the Enterprise, where Chekov is waiting. Scotty, in the meantime, has divided his time between sabotaging the Excelsior's warp drive and preparing the Enterprise for operation by a minimal crew. Kirk and the others, minus Uhura, who plans to travel to Vulcan with Sarek, steal the Enterprise from space dock. Captain Stiles and the Excelsior are ordered to pursue, but Scotty has disabled the larger ship's supposedly superior capabilities. The Enterprise continues unchecked toward Genesis. On the planet, Saavik and David follow more life form readings through a zone of Arctic cold until they hear the cries of a child, who turns out to be a very young Vulcan male. They contact the ship with a theory that the Genesis wave may have resurrected Spock. Before allowing the landing party to return, Captain Esteban tries to contact Starfleet but communications are jammed. Kruuge's ship uncloaks and attacks, and the Grissom, a small vessel meant only for scientific duties, is destroyed with a single shot, leaving David, Saavik and the young Spock marooned. Kruuge and a party of his men beam down to find them and interrogate them about the Genesis device. While trying to elude the Klingons, David reveals to Saavik that he took some shortcuts with the development of Genesis, resulting in the planet's abnormalities and a dangerous acceleration of the age of the planet as well as all life-forms present during the Genesis detonation - meaning the childlike Spock. Spock's rapid aging means that the male Vulcan's mating drive that normally strikes every seven years of adulthood will occur with greater frequency in his accelerated development and will also bring periods of instability to the planet.

The Enterprise arrives at Genesis, where it is awaited by Kruuge's Bird of Prey, which cannot fire while cloaked. Sulu detects the ship despite the cloaking device and fires before the Klingons can attack. Kruuge beams up from Genesis and takes charge of the battle. firing back at the Enterprise and destroying most of Scotty's automatic systems. Kruuge - after one of the Klingons remaining on the surface kills David - forces a grief-stricken and enraged Kirk to surrender. Kirk sets the Enterprise to self-destruct and, with the others, abandons ship and beams down to Genesis just as most of Kruuge's men board the Enterprise. Kruuge realizes what is about to happen, but not in time to save his crew. The Enterprise destroys itself and the Klingons aboard, and the debris plunges into the atmosphere of the Genesis planet as Kirk and the others do away with the Klingon guards left on the surface. Kruuge has the last remaining member of his crew beam him to the planet, where Kirk promises to give him the secrets of Genesis in exchange for beaming the others to Kruuge's ship. Kirk and Kruuge fight furiously as the planet begins to tear itself apart, and Kirk manages to kick his Klingon opponent off a cliff and beams up to the Bird of Prey. The last Klingon is taken prisoner, and the ship is set on a course for Vulcan.

Sarek and Uhura greet Kirk and the others on Vulcan, now carrying Spock's body which had, before leaving Genesis, grown to roughly the same age as it was when Spock died. McCoy and Spock are taken to the Vulcan High Priestess, who performs a dangerous ritual to return Spock's mind to his body and free McCoy from the effects of Spock's katra. The process is successful, and McCoy is restored to health. Spock, however, will have to be re-educated on Vulcan, and will never be exactly the same again. Kirk and the others decide to stay on Vulcan for a time and receive political asylum from Sarek.